Curated Optogenetic Publication Database

Search precisely and efficiently by using the advantage of the hand-assigned publication tags that allow you to search for papers involving a specific trait, e.g. a particular optogenetic switch or a host organism.

Showing 1 - 20 of 20 results
1.

Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins.

blue iLID Magnets HEK293 HeLa NIH/3T3
Nat Methods, 14 Oct 2019 DOI: 10.1038/s41592-019-0592-7 Link to full text
Abstract: Intracellular antibodies have become powerful tools for imaging, modulating and neutralizing endogenous target proteins. Here, we describe an optogenetically activated intracellular antibody (optobody) consisting of split antibody fragments and blue-light inducible heterodimerization domains. We expanded this optobody platform by generating several optobodies from previously developed intracellular antibodies, and demonstrated that photoactivation of gelsolin and β2-adrenergic receptor (β2AR) optobodies suppressed endogenous gelsolin activity and β2AR signaling, respectively.
2.

FRET-assisted photoactivation of flavoproteins for in vivo two-photon optogenetics.

blue AsLOV2 CRY2/CIB1 HeLa MDCK mouse in vivo Signaling cascade control
Nat Methods, 9 Sep 2019 DOI: 10.1038/s41592-019-0541-5 Link to full text
Abstract: Optical dimerizers have been developed to untangle signaling pathways, but they are of limited use in vivo, partly due to their inefficient activation under two-photon (2P) excitation. To overcome this problem, we developed Förster resonance energy transfer (FRET)-assisted photoactivation, or FRAPA. On 2P excitation, mTagBFP2 efficiently absorbs and transfers the energy to the chromophore of CRY2. Based on structure-guided engineering, a chimeric protein with 40% FRET efficiency was developed and named 2P-activatable CRY2, or 2paCRY2. 2paCRY2 was employed to develop a RAF1 activation system named 2paRAF. In three-dimensionally cultured cells expressing 2paRAF, extracellular signal-regulated kinase (ERK) was efficiently activated by 2P excitation at single-cell resolution. Photoactivation of ERK was also accomplished in the epidermal cells of 2paRAF-expressing mice. We further developed an mTFP1-fused LOV domain that exhibits efficient response to 2P excitation. Collectively, FRAPA will pave the way to single-cell optical control of signaling pathways in vivo.
3.

LADL: light-activated dynamic looping for endogenous gene expression control.

blue CRY2/CIB1 CRY2olig mESCs Epigenetic modification Endogenous gene expression
Nat Methods, 24 Jun 2019 DOI: 10.1038/s41592-019-0436-5 Link to full text
Abstract: Mammalian genomes are folded into tens of thousands of long-range looping interactions. The cause-and-effect relationship between looping and genome function is poorly understood, and the extent to which loops are dynamic on short time scales remains an unanswered question. Here, we engineer a new class of synthetic architectural proteins for directed rearrangement of the three-dimensional genome using blue light. We target our light-activated-dynamic-looping (LADL) system to two genomic anchors with CRISPR guide RNAs and induce their spatial colocalization via light-induced heterodimerization of cryptochrome 2 and a dCas9-CIBN fusion protein. We apply LADL to redirect a stretch enhancer (SE) away from its endogenous Klf4 target gene and to the Zfp462 promoter. Using single-molecule RNA-FISH, we demonstrate that de novo formation of the Zfp462-SE loop correlates with a modest increase in Zfp462 expression. LADL facilitates colocalization of genomic loci without exogenous chemical cofactors and will enable future efforts to engineer reversible and oscillatory loops on short time scales.
4.

Optogenetic tools light up phase separation.

blue LOV domains Review
Nat Methods, 30 Jan 2019 DOI: 10.1038/s41592-019-0310-5 Link to full text
Abstract: Abstract not available.
5.

A light-gated potassium channel for sustained neuronal inhibition.

blue AsLOV2 Cos-7 HEK293T rat hippocampal neurons rat in vivo zebrafish in vivo Neuronal activity control
Nat Methods, 30 Oct 2018 DOI: 10.1038/s41592-018-0186-9 Link to full text
Abstract: Currently available inhibitory optogenetic tools provide short and transient silencing of neurons, but they cannot provide long-lasting inhibition because of the requirement for high light intensities. Here we present an optimized blue-light-sensitive synthetic potassium channel, BLINK2, which showed good expression in neurons in three species. The channel is activated by illumination with low doses of blue light, and in our experiments it remained active over (tens of) minutes in the dark after the illumination was stopped. This activation caused long periods of inhibition of neuronal firing in ex vivo recordings of mouse neurons and impaired motor neuron response in zebrafish in vivo. As a proof-of-concept application, we demonstrated that in a freely moving rat model of neuropathic pain, the activation of a small number of BLINK2 channels caused a long-lasting (>30 min) reduction in pain sensation.
6.

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9.

blue AsLOV2 HEK293T U-2 OS Epigenetic modification Endogenous gene expression Nucleic acid editing
Nat Methods, 30 Oct 2018 DOI: 10.1038/s41592-018-0178-9 Link to full text
Abstract: Anti-CRISPR proteins are powerful tools for CRISPR-Cas9 regulation; the ability to precisely modulate their activity could facilitate spatiotemporally confined genome perturbations and uncover fundamental aspects of CRISPR biology. We engineered optogenetic anti-CRISPR variants comprising hybrids of AcrIIA4, a potent Streptococcus pyogenes Cas9 inhibitor, and the LOV2 photosensor from Avena sativa. Coexpression of these proteins with CRISPR-Cas9 effectors enabled light-mediated genome and epigenome editing, and revealed rapid Cas9 genome targeting in human cells.
7.

CRISPR-Cas9-based photoactivatable transcription systems to induce neuronal differentiation.

blue CRY2/CIB1 Magnets HEK293T HeLa human fetal fibroblasts human IPSCs Cell differentiation Endogenous gene expression
Nat Methods, 11 Sep 2017 DOI: 10.1038/nmeth.4430 Link to full text
Abstract: Our improved CRISPR-Cas9-based photoactivatable transcription systems, CPTS2.0 and Split-CPTS2.0, enable high blue-light-inducible activation of endogenous target genes in various human cell lines. We achieved reversible activation of target genes with CPTS2.0 and induced neuronal differentiation in induced pluripotent stem cells (iPSCs) by upregulating NEUROD1 with Split-CPTS2.0.
8.

Optogenetic control with a photocleavable protein, PhoCl.

violet Fluorescent proteins Background
Nat Methods, 13 Mar 2017 DOI: 10.1038/nmeth.4222 Link to full text
Abstract: To expand the range of experiments that are accessible with optogenetics, we developed a photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after violet-light-induced cleavage of a specific bond in the protein backbone. We demonstrated that PhoCl can be used to engineer light-activatable Cre recombinase, Gal4 transcription factor, and a viral protease that in turn was used to activate opening of the large-pore ion channel Pannexin-1.
9.

LOVTRAP: an optogenetic system for photoinduced protein dissociation.

blue LOVTRAP HEK293 HeLa in vitro Control of cytoskeleton / cell motility / cell shape
Nat Methods, 18 Jul 2016 DOI: 10.1038/nmeth.3926 Link to full text
Abstract: LOVTRAP is an optogenetic approach for reversible light-induced protein dissociation using protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in the dissociation constant (Kd). By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins' access to the cell edge, demonstrating a naturally occurring 3-mHz cell-edge oscillation driven by interactions of Vav2, Rac1, and PI3K proteins.
10.

A bacterial phytochrome-based optogenetic system controllable with near-infrared light.

blue near-infrared red BphP1/PpsR2 PhyB/PIF6 VVD HeLa in vitro mouse in vivo Control of cytoskeleton / cell motility / cell shape
Nat Methods, 9 May 2016 DOI: 10.1038/nmeth.3864 Link to full text
Abstract: Light-mediated control of protein-protein interactions to regulate cellular pathways is an important application of optogenetics. Here, we report an optogenetic system based on the reversible light-induced binding between the bacterial phytochrome BphP1 and its natural partner PpsR2 from Rhodopseudomonas palustris bacteria. We extensively characterized the BphP1-PpsR2 interaction both in vitro and in mammalian cells and then used this interaction to translocate target proteins to specific cellular compartments, such as the plasma membrane and the nucleus. We showed light-inducible control of cell morphology that resulted in a substantial increase of the cell area. We demonstrated light-dependent gene expression with 40-fold contrast in cultured cells, 32-fold in subcutaneous mouse tissue, and 5.7-fold in deep tissues in mice. Characteristics of the BphP1-PpsR2 optogenetic system include its sensitivity to 740- to 780-nm near-infrared light, its ability to utilize an endogenous biliverdin chromophore in eukaryotes (including mammals), and its spectral compatibility with blue-light-driven optogenetic systems.
11.

Reversible protein inactivation by optogenetic trapping in cells.

blue CRY2/CIB1 HEK293 HeLa NIH/3T3 Control of cytoskeleton / cell motility / cell shape Cell cycle control
Nat Methods, 4 May 2014 DOI: 10.1038/nmeth.2940 Link to full text
Abstract: We present a versatile platform to inactivate proteins in living cells using light, light-activated reversible inhibition by assembled trap (LARIAT), which sequesters target proteins into complexes formed by multimeric proteins and a blue light-mediated heterodimerization module. Using LARIAT, we inhibited diverse proteins that modulate cytoskeleton, lipid signaling and cell cycle with high spatiotemporal resolution. Use of single-domain antibodies extends the method to target proteins containing specific epitopes, including GFP.
12.

Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals.

green red CcaS/CcaR Cph1 E. coli
Nat Methods, 9 Mar 2014 DOI: 10.1038/nmeth.2884 Link to full text
Abstract: Gene circuits are dynamical systems that regulate cellular behaviors, often using protein signals as inputs and outputs. Here we have developed an optogenetic 'function generator' method for programming tailor-made gene expression signals in live bacterial cells. We designed precomputed light sequences based on experimentally calibrated mathematical models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time courses. We used this approach to generate accelerated and linearized dynamics, sinusoidal oscillations with desired amplitudes and periods, and a complex waveform, all with unprecedented accuracy and precision. We also combined the function generator with a dual fluorescent protein reporter system, analogous to a dual-channel oscilloscope, to reveal that a synthetic repressible promoter linearly transforms repressor signals with an approximate 7-min delay. Our approach will enable a new generation of dynamical analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.
13.

Optogenetic protein clustering and signaling activation in mammalian cells.

blue CRY2/CRY2 HEK293T NIH/3T3 Signaling cascade control Control of cytoskeleton / cell motility / cell shape
Nat Methods, 3 Feb 2013 DOI: 10.1038/nmeth.2360 Link to full text
Abstract: We report an optogenetic method based on Arabidopsis thaliana cryptochrome 2 for rapid and reversible protein oligomerization in response to blue light. We demonstrated its utility by photoactivating the β-catenin pathway, achieving a transcriptional response higher than that obtained with the natural ligand Wnt3a. We also demonstrated the modularity of this approach by photoactivating RhoA with high spatiotemporal resolution, thereby suggesting a previously unknown mode of activation for this Rho GTPase.
14.

TULIPs: tunable, light-controlled interacting protein tags for cell biology.

blue TULIP HeLa in vitro S. cerevisiae Signaling cascade control Control of cytoskeleton / cell motility / cell shape Cell cycle control
Nat Methods, 4 Mar 2012 DOI: 10.1038/nmeth.1904 Link to full text
Abstract: Naturally photoswitchable proteins offer a means of directly manipulating the formation of protein complexes that drive a diversity of cellular processes. We developed tunable light-inducible dimerization tags (TULIPs) based on a synthetic interaction between the LOV2 domain of Avena sativa phototropin 1 (AsLOV2) and an engineered PDZ domain (ePDZ). TULIPs can recruit proteins to diverse structures in living yeast and mammalian cells, either globally or with precise spatial control using a steerable laser. The equilibrium binding and kinetic parameters of the interaction are tunable by mutation, making TULIPs readily adaptable to signaling pathways with varying sensitivities and response times. We demonstrate the utility of TULIPs by conferring light sensitivity to functionally distinct components of the yeast mating pathway and by directing the site of cell polarization.
15.

Spatiotemporal control of gene expression by a light-switchable transgene system.

blue VVD HEK293 Hep G2 in vitro MCF7 MDA-MB-231 mouse in vivo PC-3 Transgene expression
Nat Methods, 12 Feb 2012 DOI: 10.1038/nmeth.1892 Link to full text
Abstract: We developed a light-switchable transgene system based on a synthetic, genetically encoded light-switchable transactivator. The transactivator binds promoters upon blue-light exposure and rapidly initiates transcription of target transgenes in mammalian cells and in mice. This transgene system provides a robust and convenient way to spatiotemporally control gene expression and can be used to manipulate many biological processes in living systems with minimal perturbation.
16.

Light-based feedback for controlling intracellular signaling dynamics.

red PhyB/PIF6 NIH/3T3 Signaling cascade control
Nat Methods, 11 Sep 2011 DOI: 10.1038/nmeth.1700 Link to full text
Abstract: The ability to apply precise inputs to signaling species in live cells would be transformative for interrogating and understanding complex cell-signaling systems. Here we report an 'optogenetic' method for applying custom signaling inputs using feedback control of a light-gated protein-protein interaction. We applied this strategy to perturb protein localization and phosphoinositide 3-kinase activity, generating time-varying signals and clamping signals to buffer against cell-to-cell variability or changes in pathway activity.
17.

Rapid blue-light-mediated induction of protein interactions in living cells.

blue CRY2/CIB1 HEK293T S. cerevisiae
Nat Methods, 31 Oct 2010 DOI: 10.1038/nmeth.1524 Link to full text
Abstract: Dimerizers allowing inducible control of protein-protein interactions are powerful tools for manipulating biological processes. Here we describe genetically encoded light-inducible protein-interaction modules based on Arabidopsis thaliana cryptochrome 2 and CIB1 that require no exogenous ligands and dimerize on blue-light exposure with subsecond time resolution and subcellular spatial resolution. We demonstrate the utility of this system by inducing protein translocation, transcription and Cre recombinase-mediated DNA recombination using light.
18.

Rationally improving LOV domain-based photoswitches.

blue AsLOV2 in vitro
Nat Methods, 20 Jun 2010 DOI: 10.1038/nmeth.1473 Link to full text
Abstract: Genetically encoded protein photosensors are promising tools for engineering optical control of cellular behavior; we are only beginning to understand how to couple these light detectors to effectors of choice. Here we report a method that increases the dynamic range of an artificial photoswitch based on the LOV2 domain of Avena sativa phototropin 1 (AsLOV2). This approach can potentially be used to improve many AsLOV2-based photoswitches.
19.

Activation of protein splicing with light in yeast.

red PhyB/PIF3 S. cerevisiae
Nat Methods, 13 Feb 2008 DOI: 10.1038/nmeth.1189 Link to full text
Abstract: Spatiotemporal regulation of protein function is a key feature of living systems; experimental tools that provide such control are of great utility. Here we report a genetically encoded system for controlling a post-translational process, protein splicing, with light. Studies in Saccharomyces cerevisiae demonstrate that fusion of a photodimerization system from Arabidopsis thaliana to an artificially split intein permits rapid activation of protein splicing to yield a new protein product.
20.

Fast manipulation of cellular cAMP level by light in vivo.

blue euPAC D. melanogaster in vivo HEK293 Xenopus oocytes Immediate control of second messengers Neuronal activity control
Nat Methods, 26 Nov 2006 DOI: 10.1038/nmeth975 Link to full text
Abstract: The flagellate Euglena gracilis contains a photoactivated adenylyl cyclase (PAC), consisting of the flavoproteins PACalpha and PACbeta. Here we report functional expression of PACs in Xenopus laevis oocytes, HEK293 cells and in Drosophila melanogaster, where neuronal expression yields light-induced changes in behavior. The activity of PACs is strongly and reversibly enhanced by blue light, providing a powerful tool for light-induced manipulation of cAMP in animal cells.
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